molecular biology primer l.
Skip this Video
Loading SlideShow in 5 Seconds..
Molecular Biology Primer PowerPoint Presentation
Download Presentation
Molecular Biology Primer

Loading in 2 Seconds...

play fullscreen
1 / 72

Molecular Biology Primer - PowerPoint PPT Presentation

  • Uploaded on

Molecular Biology Primer Angela Brooks, Raymond Brown, Calvin Chen, Mike Daly, Hoa Dinh, Erinn Hama, Robert Hinman, Julio Ng, Michael Sneddon, Hoa Troung, Jerry Wang, Che Fung Yung Outline: 0. History: Major Events in Molecular Biology 1. What Is Life Made Of?

I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
Download Presentation

PowerPoint Slideshow about 'Molecular Biology Primer' - bernad

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.

- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
molecular biology primer

Molecular Biology Primer

Angela Brooks, Raymond Brown, Calvin Chen, Mike Daly, Hoa Dinh, Erinn Hama, Robert Hinman, Julio Ng, Michael Sneddon, Hoa Troung, Jerry Wang, Che Fung Yung

  • 0. History: Major Events in Molecular Biology
  • 1. What Is Life Made Of?
  • 2. What Is Genetic Material?
  • 3. What Do Genes Do?
  • 4. What Molecule Code For Genes?
  • 5. What Is the Structure Of DNA?
  • 6. What Carries Information between DNA and Proteins
  • 7. How are Proteins Made?
outline cont
Outline Cont.
  • 8. How Can We Analyze DNA
    • 1. Copying DNA
    • 2. Cutting and Pasting DNA
    • 3. Measuring DNA Length
    • 4. Probing DNA
  • 9. How Do Individuals of a Species Differ
  • 10. How Do Different Species Differ
    • 1. Molecular Evolution
    • 2. Comparative Genomics
    • 3. Genome Rearrangement
  • 11. Why Bioinformatics?
major events in the history of molecular biology 1986 1995
Major events in the history of Molecular Biology 1986 - 1995
  • 1986 Leroy Hood: Developed automated sequencing mechanism
  • 1986 Human Genome Initiative announced
  • 1990 The 15 year Human Genome project is launched by congress
  • 1995 Moderate-resolution maps of chromosomes 3, 11, 12, and 22 maps published (These maps provide the locations of “markers” on each chromosome to make locating genes easier)

Leroy Hood

major events in the history of molecular biology 1995 1996
Major events in the history of Molecular Biology 1995-1996
  • 1995 John Craig Venter: First bactierial genomes sequenced
  • 1995 Automated fluorescent sequencing instruments and robotic operations
  • 1996 First eukaryotic genome-yeast-sequenced

John Craig Venter

major events in the history of molecular biology 1997 1999
Major events in the history of Molecular Biology 1997 - 1999
  • 1997 E. Coli sequenced
  • 1998 PerkinsElmer, Inc.. Developed 96-capillary sequencer
  • 1998 Complete sequence of the Caenorhabditis elegans genome
  • 1999 First human chromosome (number 22) sequenced
major events in the history of molecular biology 2000 2001
Major events in the history of Molecular Biology 2000-2001
  • 2000 Complete sequence of the euchromatic portion of the Drosophila melanogaster genome
  • 2001 International Human Genome Sequencing:first draft of the sequence of the human genome published
major events in the history of molecular biology 2003 present
Major events in the history of Molecular Biology 2003- Present
  • April 2003 Human Genome Project Completed. Mouse genome is sequenced.
  • April 2004 Rat genome sequenced.
life begins with cell
Life begins with Cell
  • A cell is a smallest structural unit of an organism that is capable of independent functioning
  • All cells have some common features
  • Chemical composition-by weight
    • 70% water
    • 7% small molecules
      • salts
      • Lipids
      • amino acids
      • nucleotides
    • 23% macromolecules
      • Proteins
      • Polysaccharides
      • lipids
  • biochemical (metabolic) pathways
  • translation of mRNA into proteins
all cells have common cycles
All Cells have common Cycles
  • Born, eat, replicate, and die
prokaryotes and eukaryotes
Prokaryotes and Eukaryotes
  • According to the most recent evidence, there are three main branches to the tree of life.
  • Prokaryotes include Archaea (“ancient ones”) and bacteria.
  • Eukaryotes are kingdom Eukarya and includes plants, animals, fungi and certain algae.
prokaryotes v s eukaryotes structural differences

Eubacterial (blue green algae)

and archaebacteria

only one type of membrane--

plasma membrane forms

the boundary of the cell proper

The smallest cells known are bacteria

Ecoli cell

3x106 protein molecules

1000-2000 polypeptide species.


plants, animals, Protista, and fungi

complex systems of internal membranes forms

organelle and compartments

The volume of the cell is several hundred times larger

Hela cell

5x109 protein molecules

5000-10,000 polypeptide species

Prokaryotes v.s. EukaryotesStructural differences
prokaryotic and eukaryotic cells chromosomal differences

The genome of E.coli contains amount of t 4X106 base pairs

> 90% of DNA encode protein

Lacks a membrane-bound nucleus.

Circular DNA and supercoiled


Histones are unknown


The genome of yeast cells contains

1.35x107 base pairs

A small fraction of the total DNA encodes protein.

Many repeats of non-coding sequences

All chromosomes are contained in a membrane bound nucleus

DNA is divided between two or more chromosomes

A set of five histones

DNA packaging and gene expression regulation

Prokaryotic and Eukaryotic CellsChromosomal differences
signaling pathways control gene activity
Signaling Pathways: Control Gene Activity
  • Instead of having brains, cells make decision through complex networks of chemical reactions, called pathways
    • Synthesize new materials
    • Break other materials down for spare parts
    • Signal to eat or die
cells information and machinery
Cells Information and Machinery
  • Cells store all information to replicate itself
    • Human genome is around 3 billions base pair long
    • Almost every cell in human body contains same set of genes
    • But not all genes are used or expressed by those cells
  • Machinery:
    • Collect and manufacture components
    • Carry out replication
    • Kick-start its new offspring

(A cell is like a car factory)

overview of organizations of life
Overview of organizations of life
  • Nucleus = library
  • Chromosomes = bookshelves
  • Genes = books
  • Almost every cell in an organism contains the same libraries and the same sets of books.
  • Books represent all the information (DNA) that every cell in the body needs so it can grow and carry out its vaious functions.
some terminology
Some Terminology
  • Genome: an organism’s genetic material
  • Gene: a discrete units of hereditary information located on the chromosomes and consisting of DNA.
  • Genotype: The genetic makeup of an organism
  • Phenotype: the physical expressed traits of an organism
  • Nucleic acid: Biological molecules(RNA and DNA) that allow organisms to reproduce;
more terminology
More Terminology
  • The genome is an organism’s complete set of DNA.
    • a bacteria contains about 600,000 DNA base pairs
    • human and mouse genomes have some 3 billion.
  • human genome has 24 distinct chromosomes.
    • Each chromosome contains many genes.
  • Gene
    • basic physical and functional units of heredity.
    • specific sequences of DNA bases that encode instructions on how to make proteins.
  • Proteins
    • Make up the cellular structure
    • large, complex molecules made up of smaller subunits called amino acids.
all life depends on 3 critical molecules
All Life depends on 3 critical molecules
  • DNAs
    • Hold information on how cell works
  • RNAs
    • Act to transfer short pieces of information to different parts of cell
    • Provide templates to synthesize into protein
  • Proteins
    • Form enzymes that send signals to other cells and regulate gene activity
    • Form body’s major components (e.g. hair, skin, etc.)
Central Dogma

(DNARNAprotein) The paradigm that DNA directs its transcription to RNA, which is then translated into a protein.

  • Transcription

(DNARNA) The process which transfers genetic information from the DNA to the RNA.

  • Translation

(RNAprotein) The process of transforming RNA to protein as specified by the genetic code.

central dogma of biology
Central Dogma of Biology

The information for making proteins is stored in DNA. There is a process (transcription and translation) by which DNA is converted to protein. By understanding this process and how it is regulated we can make predictions and models of cells.


Protein Sequence Analysis

Sequence analysis

Gene Finding

dna the genetics makeup
DNA the Genetics Makeup
  • Genes are inherited and are expressed
    • genotype (genetic makeup)
    • phenotype (physical expression)
  • On the left, is the eye’s phenotypes of green and black eye genes.
discovery of dna

1 Biologist

1 Physics Ph.D. Student

900 words

Nobel Prize

Discovery of DNA
  • DNA Sequences
    • Chargaff and Vischer, 1949
      • DNA consisting of A, T, G, C
        • Adenine, Guanine, Cytosine, Thymine
    • Chargaff Rule
      • Noticing #A#T and #G#C
        • A “strange but possibly meaningless” phenomenon.
  • Wow!! A Double Helix
    • Watson and Crick, Nature, April 25, 1953
    • Rich, 1973
      • Structural biologist at MIT.
      • DNA’s structure in atomic resolution.

Crick Watson

watson crick the secret of life

Watson & Crick with DNA model

Rosalind Franklin with X-ray image of DNA

Watson & Crick – “…the secret of life”
  • Watson: a zoologist, Crick: a physicist
  • “In 1947 Crick knew no biology and practically no organic chemistry or crystallography..” –
  • Applying Chagraff’s rules and the X-ray image from Rosalind Franklin, they constructed a “tinkertoy” model showing the double helix
  • Their 1953 Nature paper: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”
dna the basis of life
DNA: The Basis of Life
  • Humans have about 3 billion base pairs.
    • How do you package it into a cell?
    • How does the cell know where in the highly packed DNA where to start transcription?
      • Special regulatory sequences
    • DNA size does not mean more complex
  • Complexity of DNA
    • Eukaryotic genomes consist of variable amounts of DNA
      • Single Copy or Unique DNA
      • Highly Repetitive DNA
dna the code of life
DNA: The Code of Life
  • The structure and the four genomic letters code for all living organisms
  • Adenine, Guanine, Thymine, and Cytosine which pair A-T and C-G on complimentary strands.
dna continued
DNA, continued
  • DNA has a double helix structure which composed of
    • sugar molecule
    • phosphate group
    • and a base (A,C,G,T)
  • DNA always reads from 5’ end to 3’ end for transcription replication



genetic information chromosomes
Genetic Information: Chromosomes
  • (1) Double helix DNA strand.
  • (2) Chromatin strand (DNA with histones)
  • (3) Condensed chromatin during interphase with centromere.
  • (4) Condensed chromatin during prophase
  • (5) Chromosome during metaphase

Organism Number of base pair number of Chromosomes



Escherichia coli (bacterium) 4x106 1


Saccharomyces cerevisiae (yeast) 1.35x107 17

Drosophila melanogaster(insect) 1.65x108 4

Homo sapiens(human) 2.9x109 23

Zea mays(corn) 5.0x109 10

dna rna and the flow of information
DNA, RNA, and the Flow of Information




dna replication
DNA - replication
  • DNA can replicate by splitting, and rebuilding each strand.
  • Note that the rebuilding of each strand uses slightly different mechanisms due to the 5’ 3’ asymmetry, but each daughter strand is an exact replica of the original strand.


Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

transcriptional regulation






Transcriptional Regulation

Lodish et al. Molecular Biology of the Cell (5th ed.). W.H. Freeman & Co., 2003.

overview of dna to rna to protein
Overview of DNA to RNA to Protein
  • A gene is expressed in two steps
    • Transcription: RNA synthesis
    • Translation: Protein synthesis
cell information instruction book of life
Cell Information: Instruction book of Life
  • DNA, RNA, and Proteins are examples of strings written in either the four-letter nucleotide of DNA and RNA (A C G T/U)
  • or the twenty-letter amino acid of proteins. Each amino acid is coded by 3 nucleotides called codon. (Leu, Arg, Met, etc.)
proteins workhorses of the cell
Proteins: Workhorses of the Cell
  • 20 different amino acids
    • different chemical properties cause the protein chains to fold up into specific three-dimensional structures that define their particular functions in the cell.
  • Proteins do all essential work for the cell
    • build cellular structures
    • digest nutrients
    • execute metabolic functions
    • Mediate information flow within a cell and among cellular communities.
  • Proteins work together with other proteins or nucleic acids as "molecular machines"
    • structures that fit together and function in highly specific, lock-and-key ways.
  • RNA is similar to DNA chemically. It is usually only a single strand. T(hyamine) is replaced by U(racil)
  • Some forms of RNA can form secondary structures by “pairing up” with itself. This can have change its properties dramatically.


can pair with

each other.

tRNA linear and 3D view:

rna continued
RNA, continued
  • Several types exist, classified by function
  • mRNA – this is what is usually being referred to when a Bioinformatician says “RNA”. This is used to carry a gene’s message out of the nucleus.
  • tRNA – transfers genetic information from mRNA to an amino acid sequence
  • rRNA – ribosomal RNA. Part of the ribosome which is involved in translation.
terminology for transcription
Terminology for Transcription
  • hnRNA (heterogeneous nuclear RNA): Eukaryotic mRNA primary transcipts whose introns have not yet been excised (pre-mRNA).
  • Phosphodiester Bond: Esterification linkage between a phosphate group and two alcohol groups.
  • Promoter: A special sequence of nucleotides indicating the starting point for RNA synthesis.
  • RNA (ribonucleotide): Nucleotides A,U,G, and C with ribose
  • RNA Polymerase II: Multisubunit enzyme that catalyzes the synthesis of an RNA molecule on a DNA template from nucleoside triphosphate precursors.
  • Terminator: Signal in DNA that halts transcription.
  • The process of making RNA from DNA
  • Catalyzed by “transcriptase” enzyme
  • Needs a promoter region to begin transcription.
  • ~50 base pairs/second in bacteria, but multiple transcriptions can occur simultaneously

dna rna transcription
DNA  RNA: Transcription
  • DNA gets transcribed by a protein known as RNA-polymerase
  • This process builds a chain of bases that will become mRNA
  • RNA and DNA are similar, except that RNA is single stranded and thus less stable than DNA
    • Also, in RNA, the base uracil (U) is used instead of thymine (T), the DNA counterpart
transcription continued
Transcription, continued
  • Transcription is highly regulated. Most DNA is in a dense form where it cannot be transcribed.
  • To begin transcription requires a promoter, a small specific sequence of DNA to which polymerase can bind (~40 base pairs “upstream” of gene)
  • Finding these promoter regions is a partially solved problem that is related to motif finding.
  • There can also be repressors and inhibitors acting in various ways to stop transcription. This makes regulation of gene transcription complex to understand.
definition of a gene
Definition of a Gene
  • Regulatory regions: up to 50 kb upstream of +1 site
  • Exons: protein coding and untranslated regions (UTR)

1 to 178 exons per gene (mean 8.8)

8 bp to 17 kb per exon (mean 145 bp)

  • Introns: splice acceptor and donor sites, junk DNA

average 1 kb – 50 kb per intron

  • Gene size: Largest – 2.4 Mb (Dystrophin). Mean – 27 kb.
transcription dna hnrna
Transcription: DNA  hnRNA
  • Transcription occurs in the nucleus.
  • σ factor from RNA polymerase reads the promoter sequence and opens a small portion of the double helix exposing the DNA bases.
  • RNA polymerase II catalyzes the formation of phosphodiester bond that link nucleotides together to form a linear chain from 5’ to 3’ by unwinding the helix just ahead of the active site for polymerization of complementary base pairs.
  • The hydrolysis of high energy bonds of the substrates (nucleoside triphosphates ATP, CTP, GTP, and UTP) provides energy to drive the reaction.
  • During transcription, the DNA helix reforms as RNA forms.
  • When the terminator sequence is met, polymerase halts and releases both the DNA template and the RNA.
central dogma revisited
Central Dogma Revisited



  • Base Pairing Rule: A and T or U is held together by 2 hydrogen bonds and G and C is held together by 3 hydrogen bonds.
  • Note: Some mRNA stays as RNA (ie tRNA,rRNA).








Ribosome in Cytoplasm

terminology for splicing
Terminology for Splicing
  • Exon: A portion of the gene that appears in both the primary and the mature mRNA transcripts.
  • Intron: A portion of the gene that is transcribed but excised prior to translation.
  • Lariat structure: The structure that an intron in mRNA takes during excision/splicing.
  • Spliceosome: A organelle that carries out the splicing reactions whereby the pre-mRNA is converted to a mature mRNA.
splicing hnrna mrna
Splicing: hnRNA  mRNA
  • Takes place on spliceosome that brings together a hnRNA, snRNPs, and a variety of pre-mRNA binding proteins.
  • 2 transesterification reactions:
  • 2’,5’ phosphodiester bond forms between an intron adenosine residue and the intron’s 5’-terminal phosphate group and a lariat structure is formed.
  • The free 3’-OH group of the 5’ exon displaces the 3’ end of the intron, forming a phosphodiester bond with the 5’ terminal phosphate of the 3’ exon to yield the spliced product. The lariat formed intron is the degraded.
splicing and other rna processing
Splicing and other RNA processing
  • In Eukaryotic cells, RNA is processed between transcription and translation.
  • This complicates the relationship between a DNA gene and the protein it codes for.
  • Sometimes alternate RNA processing can lead to an alternate protein as a result. This is true in the immune system.
splicing eukaryotes
Splicing (Eukaryotes)
  • Unprocessed RNA is composed of Introns and Extrons. Introns are removed before the rest is expressed and converted to protein.
  • Sometimes alternate splicings can create different valid proteins.
  • A typical Eukaryotic gene has 4-20 introns. Locating them by analytical means is not easy.
terminology for ribosome
Terminology for Ribosome
  • Codon: The sequence of 3 nucleotides in DNA/RNA that encodes for a specific amino acid.
  • mRNA (messenger RNA): A ribonucleic acid whose sequence is complementary to that of a protein-coding gene in DNA.
  • Ribosome: The organelle that synthesizes polypeptides under the direction of mRNA
  • rRNA (ribosomal RNA):The RNA molecules that constitute the bulk of the ribosome and provides structural scaffolding for the ribosome and catalyzes peptide bond formation.
  • tRNA (transfer RNA): The small L-shaped RNAs that deliver specific amino acids to ribosomes according to the sequence of a bound mRNA.
mrna ribosome
mRNA  Ribosome
  • mRNA leaves the nucleus via nuclear pores.
  • Ribosome has 3 binding sites for tRNAs:
    • A-site: position that aminoacyl-tRNA molecule binds to vacant site
    • P-site: site where the new peptide bond is formed.
    • E-site: the exit site
  • Two subunits join together on a mRNA molecule near the 5’ end.
  • The ribosome will read the codons until AUG is reached and then the initiator tRNA binds to the P-site of the ribosome.
  • Stop codons have tRNA that recognize a signal to stop translation. Release factors bind to the ribosome which cause the peptidyl transferase to catalyze the addition of water to free the molecule and releases the polypeptide.
terminology for trna and proteins
Terminology for tRNA and proteins
  • Anticodon: The sequence of 3 nucleotides in tRNA that recognizes an mRNA codon through complementary base pairing.
  • C-terminal: The end of the protein with the free COOH.
  • N-terminal: The end of the protein with the free NH3.
purpose of trna
Purpose of tRNA
  • The proper tRNA is chosen by having the corresponding anticodon for the mRNA’s codon.
  • The tRNA then transfers its aminoacyl group to the growing peptide chain.
  • For example, the tRNA with the anticodon UAC corresponds with the codon AUG and attaches methionine amino acid onto the peptide chain.
rna protein translation
RNA  Protein: Translation
  • Ribosomes and transfer-RNAs (tRNA) run along the length of the newly synthesized mRNA, decoding one codon at a time to build a growing chain of amino acids (“peptide”)
    • The tRNAs have anti-codons, which complimentarily match the codons of mRNA to know what protein gets added next
  • But first, in eukaryotes, a phenomenon called splicing occurs
    • Introns are non-protein coding regions of the mRNA; exons are the coding regions
    • Introns are removed from the mRNA during splicing so that a functional, valid protein can form
  • The process of going from RNA to polypeptide.
  • Three base pairs of RNA (called a codon) correspond to one amino acid based on a fixed table.
  • Always starts with Methionine and ends with a stop codon
translation continued
Translation, continued
  • Catalyzed by Ribosome
  • Using two different sites, the Ribosome continually binds tRNA, joins the amino acids together and moves to the next location along the mRNA
  • ~10 codons/second, but multiple translations can occur simultaneously

protein synthesis summary
Protein Synthesis: Summary
  • There are twenty amino acids, each coded by three- base-sequences in DNA, called “codons”
    • This code is degenerate
  • The central dogma describes how proteins derive from DNA
    • DNA mRNA  (splicing?)  protein
  • The protein adopts a 3D structure specific to it’s amino acid arrangement and function
  • Complex organic molecules made up of amino acid subunits
  • 20* different kinds of amino acids. Each has a 1 and 3 letter abbreviation.
  • for complete list of chemical structures and abbreviations.
  • Proteins are often enzymes that catalyze reactions.
  • Also called “poly-peptides”

*Some other amino acids exist but not in humans.

polypeptide v protein
Polypeptide v. Protein
  • A protein is a polypeptide, however to understand the function of a protein given only the polypeptide sequence is a very difficult problem.
  • Protein folding an open problem. The 3D structure depends on many variables.
  • Current approaches often work by looking at the structure of homologous (similar) proteins.
  • Improper folding of a protein is believed to be the cause of mad cow disease. for more information on folding

protein folding
Protein Folding
  • Proteins tend to fold into the lowest free energy conformation.
  • Proteins begin to fold while the peptide is still being translated.
  • Proteins bury most of its hydrophobic residues in an interior core to form an α helix.
  • Most proteins take the form of secondary structures α helices and β sheets.
  • Molecular chaperones, hsp60 and hsp 70, work with other proteins to help fold newly synthesized proteins.
  • Much of the protein modifications and folding occurs in the endoplasmic reticulum and mitochondria.
protein folding68
Protein Folding
  • Proteins are not linear structures, though they are built that way
  • The amino acids have very different chemical properties; they interact with each other after the protein is built
    • This causes the protein to start fold and adopting it’s functional structure
    • Proteins may fold in reaction to some ions, and several separate chains of peptides may join together through their hydrophobic and hydrophilic amino acids to form a polymer
protein folding cont d
Protein Folding (cont’d)
  • The structure that a protein adopts is vital to it’s chemistry
  • Its structure determines which of its amino acids are exposed carry out the protein’s function
  • Its structure also determines what substrates it can react with
  • The DNA can be thought of as a sequence of the nucleotides: C,A,G, or T.
  • What happens to genes when the DNA sequence is mutated?


Normal DNA sequence:

Mutated DNA sequence:



the good the bad and the silent
The Good, the Bad, and the Silent
  • Mutations can serve the organism in three ways:
  • The Good :
  • The Bad :
  • The Silent:

A mutation can cause a trait that enhances the organism’s function:

Mutation in the sickle cell gene provides resistance to malaria.

A mutation can cause a trait that is harmful, sometimes fatal to the organism:

Huntington’s disease, a symptom of a gene mutation, is a degenerative disease of the nervous system.

A mutation can simply cause no difference in the function of the organism.

Campbell, Biology, 5th edition, p. 255

animation video
Animation Video
  • Transcription animation (Thanks to Ajith Harish!)
    • Check out this website:
      • Chose "Copying the Code" toward the bottom of the screen
      • then select "puting it together" from the top of the next screen.
      • Then choose the "Transcription animation"
    • The parent site has a lot more stuff
  • More animations can be found at

    • In particular, check out the animations under “Transcription and Translation”, e.g., the following